This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Given a Multiple Sequence Alignment (MSA) of a family of proteins we want to find evolutionarily conserved and covarying residues, which we believe would be functionally and structurally important. Specifically we propose to elicit the structure of a Markov Random Field from the MSA, and study this structure in terms of it's ability to discriminate sequences of this family from others and also to generate new sequences which are functionally and structurally identical to ones in the family.